---
title: "COVID-19 Pandemic"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    social: menu
    source_code: embed
---

```{r setup, include=FALSE}
library(dygraphs)
library(xts)
library(lubridate)
library(dplyr)
library(tidyr)

### Data sources: 
### Our World In Data https://ourworldindata.org/coronavirus 
### Johns Hopkins Coronavirus Resource Center https://github.com/govex/COVID-19/tree/master/data_tables/vaccine_data/global_data 

covid <- read.csv(url("https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv"))

uk_covid <- covid %>%
  filter(location == "United Kingdom")

hun_covid <- covid %>%
  filter(location == "Hungary")


vax <- read.csv(url("https://raw.githubusercontent.com/govex/COVID-19/master/data_tables/vaccine_data/global_data/time_series_covid19_vaccine_global.csv"))

hun_vax <- vax %>%
  filter(Country_Region == "Hungary")
```


United Kingdom
=======================================================================

Row
-----------------------------------------------------------------------

### New cases

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 7:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_cases, order.by = uk_covid_sub$date)
names(data) <- c("New cases")
data <- abs(data$`New cases`)
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New tests

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 27:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_tests, order.by = uk_covid_sub$date)
names(data) <- c("New tests")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

Row
-----------------------------------------------------------------------

### Hospital patients

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 21:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$hosp_patients, order.by = uk_covid_sub$date)
names(data) <- c("Hospital patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### ICU patients

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 19:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$icu_patients, order.by = uk_covid_sub$date)
names(data) <- c("ICU patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 10:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_deaths, order.by = uk_covid_sub$date)
names(data) <- c("New deaths")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths per million

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 16:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_deaths_per_million, order.by = uk_covid_sub$date)
names(data) <- c("New deaths per million")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

Row
-----------------------------------------------------------------------

### People partially vaccinated (1st dose)

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 40:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$people_vaccinated, order.by = uk_covid_sub$date)
names(data) <- c("People partially vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

### People fully vaccinated (2nd dose)

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 40:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$people_fully_vaccinated, order.by = uk_covid_sub$date)
names(data) <- c("People fully vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


Hungary
=======================================================================

Row
-----------------------------------------------------------------------

### New cases

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 7:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_cases, order.by = hun_covid_sub$date)
names(data) <- c("New cases")
data <- abs(data$`New cases`)
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New tests

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 27:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_tests, order.by = hun_covid_sub$date)
names(data) <- c("New tests")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

Row
-----------------------------------------------------------------------

### Hospital patients

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 21:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$hosp_patients, order.by = hun_covid_sub$date)
names(data) <- c("Hospital patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### ICU patients (no data available)

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 19:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$icu_patients, order.by = hun_covid_sub$date)
names(data) <- c("ICU patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 10:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_deaths, order.by = hun_covid_sub$date)
names(data) <- c("New deaths")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths per million

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 16:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_deaths_per_million, order.by = hun_covid_sub$date)
names(data) <- c("New deaths per million")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


Row
-----------------------------------------------------------------------

### People partially vaccinated (1st dose)

```{r, include=FALSE}
hun_vax$Date <- ymd(hun_vax$Date)

str(hun_vax)

data <- xts(x = hun_vax$People_partially_vaccinated, order.by = hun_vax$Date)
names(data) <- c("People partially vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

### People fully vaccinated (2nd dose)

```{r, include=FALSE}
hun_vax$Date <- ymd(hun_vax$Date)

str(hun_vax)

data <- xts(x = hun_vax$People_fully_vaccinated, order.by = hun_vax$Date)
names(data) <- c("People fully vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```